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gene fusion feature request.

2 comment

Hi, Sigven, Now PCGR can analysis SNV/INDEl and CNA. would you like to add gene fusion function in the future? Another question is that given tumor/normal raw data(fastq), can you...

enhancement

config json file

hello, where to download and config these fields ? "general":{ "sequencingAdapter": "/path/to/adapters.fa", "jsvmBetaBinParams": "/path/to/jsvm_beta_bin_params.cfg", "jsvmBetaBinPriors": "/path/to/jsvm_beta_bin_priors.cfg", "jsvm_0.7.5_jointPriors": "/path/to/joint_priors.cfg", "jsvm_0.7.5_jointParams": "/path/to/joint_params.cfg", "adaclassifier_snp": "/path/to/IS3A.MVJSD.sSNV.tsv.Classifier.RData", "adaclassifier_indel": "/path/to/IS3A.MVJSD.sINDEL.tsv.Classifier.RData" } thanks !

INDELs VEP anntotation Consequence is missense_variant

2 comment

https://github.com/bm2-lab/pTuneos/blob/e6cfd0e1b57bf04fe60baee40efe4f3b0c8d56f3/src/core/VariantCallingFormat/VCFprocessor.py#L72 For INDELs, it seems that no Consequence is missense_variant ?

question